Does anyone know what the best/fastest way is to create an annoted bacterial genome assembly (genbank format) starting from a fasta file containing the whole genome sequence? (There is a gff3 file with the gene annotations available.)Thank you.
You could use something like RATT but I think this requires that the genomes be very very similar, which it sounds like yours might not be. In which case, you can still use prokka, and provide a database of 'trusted' proteins from which to start the annotation.